Hyperspectral visualization of mass spectrometry imaging data

Judith M Fonville, Claire L Carter, Luis Pizarro, Rory T Steven, Andrew D Palmer, Rian L Griffiths, Patricia F Lalor, John C Lindon, Jeremy K Nicholson, Elaine Holmes, Josephine Bunch

Research output: Contribution to journalArticlepeer-review

63 Citations (Scopus)


The acquisition of localized molecular spectra with mass spectrometry imaging (MSI) has a great, but as yet not fully realized, potential for biomedical diagnostics and research. The methodology generates a series of mass spectra from discrete sample locations, which is often analyzed by visually interpreting specifically selected images of individual masses. We developed an intuitive color-coding scheme based on hyperspectral imaging methods to generate a single overview image of this complex data set. The image color-coding is based on spectral characteristics, such that pixels with similar molecular profiles are displayed with similar colors. This visualization strategy was applied to results of principal component analysis, self-organizing maps and t-distributed stochastic neighbor embedding. Our approach for MSI data analysis, combining automated data processing, modeling and display, is user-friendly and allows both the spatial and molecular information to be visualized intuitively and effectively.
Original languageEnglish
Pages (from-to)1415-1423
Number of pages9
JournalAnalytical Chemistry
Issue number3
Publication statusPublished - 5 Feb 2013

Bibliographical note

Copyright 2013 Elsevier B.V., All rights reserved.


  • Animals
  • Brain
  • Humans
  • Liver
  • Mass Spectrometry
  • Rats
  • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization


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